The surface topography of engineered extracellular matrices is one of the most important physical cues regulating the phenotypic polarization of macrophages. However, not much is known about the ways through which submicron (i.e., 100–1000 nm) topographies modulate the polarization of macrophages. In the context of bone tissue regeneration, it is well established that this range of topographies stimulates the osteogenic differentiation of stem cells. Since the immune response affects the bone tissue regeneration process, the immunomodulatory consequences of submicron patterns should be studied prior to their clinical application. Here, we 3D printed submicron pillars (using two-photon polymerization technique) with different heights and interspacings to perform the first ever systematic study of such effects. Among the studied patterns, the highest degree of elongation was observed for the cells cultured on those with the tallest and densest pillars. After 3 days of culture with inflammatory stimuli (LPS/IFN-γ), sparsely decorated surfaces inhibited the expression of the pro-inflammatory cellular marker CCR7 as compared to day 1 and to the other patterns. Furthermore, sufficiently tall pillars polarized the M1 macrophages towards a pro-healing (M2) phenotype, as suggested by the expression of CD206 within the first 3 days. As some of the studied patterns are known to be osteogenic, the osteoimmunomodulatory capacity of the patterns should be further studied to optimize their bone tissue regeneration performance.